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International Journal of Infectious... Sep 2022To explore household transmissibility of SARS-CoV-2 in children in new-variants dominating periods. (Meta-Analysis)
Meta-Analysis Review
OBJECTIVES
To explore household transmissibility of SARS-CoV-2 in children in new-variants dominating periods.
METHODS
Through retrieval in PubMed and Embase, studies were included in two parts: meta-analysis of the household secondary attack rate (SAR) and case analysis of household pediatric infections.
RESULTS
A total of 95 articles were included: 48 for meta-analysis and 47 for case analysis. Pediatric COVID-19 only comprised a minority of the household transmission. The total pooled household SAR of child index cases and contacts were 0.20 (95% confidence interval [CI]: 0.15-0.26) and 0.24 (95% CI: 0.18-0.30). Lower household transmissibility was reported in both child index cases and contacts than in adults (relative risk [RR] = 0.64, 95% CI: 0.50-0.81; RR = 0.74, 95% CI: 0.64-0.85). Younger children were as susceptible as the older children (RR = 0.89, 95% CI: 0.72-1.10). Through subgroup analyses of different variants and periods, increased household SAR was observed in children (Wild: 0.20; Alpha: 0.42; Delta: 0.35; Omicron: 0.56), and no significant difference was found in household SAR between children and adults when new variants dominated.
CONCLUSION
Although children were found not to be dominant in the household transmission, their transmissibility of SARS-CoV-2 appeared to be on the rise as new variants emerged.
Topics: Adolescent; Adult; COVID-19; Child; Family; Family Characteristics; Humans; Incidence; SARS-CoV-2
PubMed: 35562045
DOI: 10.1016/j.ijid.2022.05.016 -
Frontiers in Microbiology 2022Due to global warming, shorter ice cover duration might drastically affect the ecology of lakes currently undergoing seasonal surface freezing. High-mountain lakes show...
Due to global warming, shorter ice cover duration might drastically affect the ecology of lakes currently undergoing seasonal surface freezing. High-mountain lakes show snow-rich ice covers that determine contrasting conditions between ice-off and ice-on periods. We characterized the bacterioplankton seasonality in a deep high-mountain lake ice-covered for half a year. The lake shows a rich core bacterioplankton community consisting of three components: (i) an assemblage stable throughout the year, dominated by Actinobacteria, resistant to all environmental conditions; (ii) an ice-on-resilient assemblage dominating during the ice-covered period, which is more diverse than the other components and includes a high abundance of Verrucomicrobia; the deep hypolimnion constitutes a refuge for many of the typical under-ice taxa, many of which recover quickly during autumn mixing; and (iii) an ice-off-resilient assemblage, which members peak in summer in epilimnetic waters when the rest decline, characterized by a dominance of , and . The rich core community and low random elements compared to other relatively small cold lakes can be attributed to its simple hydrological network in a poorly-vegetated catchment, the long water-residence time ( 4 years), and the long ice-cover duration; features common to many headwater deep high-mountain lakes.
PubMed: 36187988
DOI: 10.3389/fmicb.2022.935378 -
Korean Journal of Ophthalmology : KJO Jun 2022To investigate the characteristics and distribution of ocular dominance in primary open-angle glaucoma eyes. In addition, we tried to catch any trend of ocular dominance...
PURPOSE
To investigate the characteristics and distribution of ocular dominance in primary open-angle glaucoma eyes. In addition, we tried to catch any trend of ocular dominance according to the stage of disease.
METHODS
Two hundred participants with bilateral open-angle glaucoma underwent ocular dominant testing by "the hole-ina-card" test. Using optical coherence tomography, macular ganglion cell-inner plexiform layer, as well as circumpapillary retinal nerve fiber layer thickness were measured and compared according to ocular dominance. Of the two eyes of one subject, the eye with less glaucomatous damage based on mean deviation was considered to be the "better eye" in our study.
RESULTS
Ocular dominance was in the right eye in 66% of the population and ocular dominance was positioned in the better eye in 70% of the population (p = 0.001 and p = 0.002, respectively). In conditional logistic regression analyses, right eye and better mean deviation were significantly associated with ocular dominance (p = 0.001 and p = 0.002, respectively). Ocular dominance tends to be present in the better eye and this trend was more apparent as the severity of glaucoma increased. Intereye comparison of visual field indices and retinal nerve fiber layer thickness between dominant versus nondominant eye become apparent in moderate and advanced glaucoma whereas it was not as apparent in early glaucoma.
CONCLUSIONS
In glaucomatous eyes, laterality and severity of glaucoma determined ocular dominance. Intereye difference between nondominant and dominant eyes increased with the severity of glaucoma. Our findings suggest the existence of potential reciprocal interactions between ocular dominance and glaucoma.
Topics: Dominance, Ocular; Glaucoma; Glaucoma, Open-Angle; Humans; Intraocular Pressure; Nerve Fibers; Retinal Ganglion Cells; Tomography, Optical Coherence; Visual Field Tests
PubMed: 35176838
DOI: 10.3341/kjo.2021.0165 -
Mathematical Biosciences and... Mar 2021Active fluids consume fuel at the microscopic scale, converting this energy into forces that can drive macroscopic motions over scales far larger than their microscopic...
Active fluids consume fuel at the microscopic scale, converting this energy into forces that can drive macroscopic motions over scales far larger than their microscopic constituents. In some cases, the mechanisms that give rise to this phenomenon have been well characterized, and can explain experimentally observed behaviors in both bulk fluids and those confined in simple stationary geometries. More recently, active fluids have been encapsulated in viscous drops or elastic shells so as to interact with an outer environment or a deformable boundary. Such systems are not as well understood. In this work, we examine the behavior of droplets of an active nematic fluid. We study their linear stability about the isotropic equilibrium over a wide range of parameters, identifying regions in which different modes of instability dominate. Simulations of their full dynamics are used to identify their nonlinear behavior within each region. When a single mode dominates, the droplets behave simply: as rotors, swimmers, or extensors. When parameters are tuned so that multiple modes have nearly the same growth rate, a pantheon of modes appears, including zigzaggers, washing machines, wanderers, and pulsators.
PubMed: 33892575
DOI: 10.3934/mbe.2021145 -
The New Phytologist Oct 2019A crucial step in the transition from outcrossing to self-fertilization is the loss of genetic self-incompatibility (SI). In the Brassicaceae, SI involves the...
A crucial step in the transition from outcrossing to self-fertilization is the loss of genetic self-incompatibility (SI). In the Brassicaceae, SI involves the interaction of female and male specificity components, encoded by the genes SRK and SCR at the self-incompatibility locus (S-locus). Theory predicts that S-linked mutations, and especially dominant mutations in SCR, are likely to contribute to loss of SI. However, few studies have investigated the contribution of dominant mutations to loss of SI in wild plant species. Here, we investigate the genetic basis of loss of SI in the self-fertilizing crucifer species Capsella orientalis, by combining genetic mapping, long-read sequencing of complete S-haplotypes, gene expression analyses and controlled crosses. We show that loss of SI in C. orientalis occurred < 2.6 Mya and maps as a dominant trait to the S-locus. We identify a fixed frameshift deletion in the male specificity gene SCR and confirm loss of male SI specificity. We further identify an S-linked small RNA that is predicted to cause dominance of self-compatibility. Our results agree with predictions on the contribution of dominant S-linked mutations to loss of SI, and thus provide new insights into the molecular basis of mating system transitions.
Topics: Base Sequence; Capsella; Crosses, Genetic; Frameshift Mutation; Gene Expression Regulation, Plant; Genes, Dominant; Genetic Loci; Haplotypes; Phylogeny; Quantitative Trait, Heritable; RNA, Plant; Reproduction; Self-Incompatibility in Flowering Plants; Time Factors
PubMed: 31254395
DOI: 10.1111/nph.16035 -
Journal of the Royal Society, Interface Jan 2021We study the evolutionary dynamics of the Prisoner's Dilemma game in which cooperators and defectors interact with another actor type called exiters. Rather than being...
We study the evolutionary dynamics of the Prisoner's Dilemma game in which cooperators and defectors interact with another actor type called exiters. Rather than being exploited by defectors, exiters exit the game in favour of a small pay-off. We find that this simple extension of the game allows cooperation to flourish in well-mixed populations when iterations or reputation are added. In networked populations, however, the exit option is less conducive to cooperation. Instead, it enables the coexistence of cooperators, defectors, and exiters through cyclic dominance. Other outcomes are also possible as the exit pay-off increases or the network structure changes, including network-wide oscillations in actor abundances that may cause the extinction of exiters and the domination of defectors, although game parameters should favour exiting. The complex dynamics that emerges in the wake of a simple option to exit the game implies that nuances matter even if our analyses are restricted to incentives for rational behaviour.
Topics: Biological Evolution; Cooperative Behavior; Game Theory
PubMed: 33435841
DOI: 10.1098/rsif.2020.0777 -
Scientific Reports Mar 2022When our eyes are confronted with discrepant images (yielding incompatible retinal inputs) interocular competition (IOC) is instigated. During IOC, one image temporarily...
When our eyes are confronted with discrepant images (yielding incompatible retinal inputs) interocular competition (IOC) is instigated. During IOC, one image temporarily dominates perception, while the other is suppressed. Many factors affecting IOC have been extensively examined. One factor that received surprisingly little attention, however, is the stimulus' visual hemifield (VHF) of origin. This is remarkable, as the VHF location of stimuli is known to affect visual performance in various contexts. Prompted by exploratory analyses, we examined five independent datasets of breaking continuous flash suppression experiments, to establish the VHF's role in IOC. We found that targets presented in nasal VHF locations broke through suppression much faster than targets in temporal VHF locations. Furthermore, we found that the magnitude of this nasal advantage depended on how strongly the targets were suppressed: the nasal advantage was larger for the recessive eye than for the dominant eye, and was larger in observers with a greater dominance imbalance between the eyes. Our findings suggest that the nasal advantage reported here originates in processing stages where IOC is resolved. Finally, we propose that a nasal advantage in IOC serves an adaptive role in human vision, as it can aid perception of partially occluded objects.
Topics: Attention; Humans; Photic Stimulation; Retina; Vision, Binocular; Visual Fields; Visual Perception
PubMed: 35301373
DOI: 10.1038/s41598-022-08473-w -
Applied and Environmental Microbiology Sep 2021In the environment, nutrients are rarely available in a constant supply. Therefore, microorganisms require strategies to compete for limiting nutrients. In freshwater...
In the environment, nutrients are rarely available in a constant supply. Therefore, microorganisms require strategies to compete for limiting nutrients. In freshwater systems, ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) compete with heterotrophic bacteria, photosynthetic microorganisms, and each other for ammonium, which AOA and AOB utilize as their sole source of energy and nitrogen. We investigated the competition between highly enriched cultures of AOA (AOA-AC1) and AOB (AOB-G5-7) for ammonium. Based on the gene, the newly enriched archaeal ammonia oxidizer in AOA-AC1 was closely related to spp., and the bacterial ammonia oxidizer in AOB-G5-7, sp. strain Is79, belonged to the Nitrosomonas oligotropha group ( cluster 6a). Growth experiments in batch cultures showed that AOB-G5-7 had higher growth rates than AOA-AC1 at higher ammonium concentrations. During chemostat competition experiments under ammonium-limiting conditions, AOA-AC1 dominated the cultures, while AOB-G5-7 decreased in abundance. In batch cultures, the outcome of the competition between AOA and AOB was determined by the initial ammonium concentrations. AOA-AC1 was the dominant ammonia oxidizer at an initial ammonium concentration of 50 μM, and AOB-G5-7 was dominant at 500 μM. These findings indicate that during direct competition, AOA-AC1 was able to use ammonium that was unavailable to AOB-G5-7, while AOB-G5-7 dominated at higher ammonium concentrations. The results are in strong accordance with environmental survey data suggesting that AOA are mainly responsible for ammonia oxidation under more oligotrophic conditions, whereas AOB dominate under eutrophic conditions. Nitrification is an important process in the global nitrogen cycle. The first step, ammonia oxidation to nitrite, can be carried out by ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). In many natural environments, these ammonia oxidizers coexist. Therefore, it is important to understand the population dynamics in response to increasing ammonium concentrations. Here, we study the competition between AOA and AOB enriched from freshwater systems. The results demonstrate that AOA are more abundant in systems with low ammonium availabilities and that AOB are more abundant when the ammonium availability increases. These results will help to predict potential shifts in the community composition of ammonia oxidizers in the environment due to changes in ammonium availability.
Topics: Ammonia; Archaea; Fresh Water; Microbial Interactions; Nitrosomonas; Oxidation-Reduction; Phylogeny
PubMed: 34347515
DOI: 10.1128/AEM.01038-21 -
Pathogens (Basel, Switzerland) Sep 2021is next to the most isolated pathogen from the airways of cystic fibrosis (CF) patients, who are often infected by a dominant clone for extended periods. To be able... (Review)
Review
is next to the most isolated pathogen from the airways of cystic fibrosis (CF) patients, who are often infected by a dominant clone for extended periods. To be able to persist, the pathogen has to adapt to the hostile niche of the airways to counteract host defence, antibiotic therapy and the competition with coinfecting pathogens. is equipped with many virulence factors including adhesins, toxins that are localized on the chromosome, on plasmids or are phage-related. is especially versatile and adaptation and evolution of the pathogen occurs by the acquisition of new genes by horizontal gene transfer (HGT), changes in nucleotides (single nucleotide variations, SNVs) that can cause a selective advantage for the bacteria and become fixed in subpopulations. Methicillin-resistant are a special threat to CF patients due to the more severe lung disease occurring in infected patients. Today, with decreasing costs for sequencing, more and more studies using isolates cultured from CF patients are being published, which use whole genome sequencing (WGS), multilocus sequence typing (MLST) or -sequence typing (-typing) to follow the population dynamics of , elucidate the underlying mechanisms of phenotypic variants, newly acquired resistance or adaptation to the host response in this particular niche. In the first part of this review, an introduction to the genetic make-up and the pathogenesis of with respect to CF is provided. The second part presents an overview of recent studies and their findings using genotypic methods such as single or multilocus sequencing and whole genome sequencing, which identify factors contributing to the adaptation of and its evolution in the airways of individuals with CF.
PubMed: 34578208
DOI: 10.3390/pathogens10091177 -
ISME Communications Aug 2022Multiple carbapenem-resistant Klebsiella pneumoniae (CRKP) clones typically co-exist in hospital wards, but often certain clones will dominate. The factors driving this...
Multiple carbapenem-resistant Klebsiella pneumoniae (CRKP) clones typically co-exist in hospital wards, but often certain clones will dominate. The factors driving this dominance are largely unclear. This study began from a genomic epidemiology analysis and followed by multiple approaches to identify the potential mechanisms driving the successful spread of a dominant clone. 638 patients in a 50-bed ICU were screened. 171 (26.8%) and 21 had CRKP from swabs and clinical specimens, respectively. Many (39.8% of those with ≥7-day ICU stay) acquired CRKP. After removing 18 unable to recover, 174 CRKP isolates were genome sequenced and belonged to six sequence types, with ST11 being the most prevalent (n = 154, 88.5%) and most (n = 169, 97.1%) carrying bla. The 154 ST11 isolates belonged to 7 clones, with one (clone 1, KL64 capsular type) being dominant (n = 130, 84.4%). Clone 1 and the second-most common clone (clone 2, KL64, n = 15, 9.7%) emerged simultaneously, which was also detected by genome-based dating. Clone 1 exhibited decreased biofilm formation, shorter environment survival, and attenuated virulence. In murine gut, clone 1 outcompeted clone 2. Transcriptomic analysis showed significant upregulation of the ethanolamine operon in clone 1 when competing with clone 2. Clone 1 exhibited increased utilization of ethanolamine as a nitrogen source. This highlights that reduced virulence and enhanced ability to utilize ethanolamine may promote the success of nosocomial multidrug-resistant clones.
PubMed: 37938732
DOI: 10.1038/s43705-022-00163-y